Align Sugar-phosphatase AraL; EC 3.1.3.23; Arabinose operon protein AraL; Phosphoserine phosphatase; EC 3.1.3.3 (uncharacterized)
to candidate CA265_RS10200 CA265_RS10200 HAD family hydrolase
Query= curated2:P94526 (272 letters) >FitnessBrowser__Pedo557:CA265_RS10200 Length = 260 Score = 115 bits (287), Expect = 1e-30 Identities = 76/250 (30%), Positives = 122/250 (48%), Gaps = 5/250 (2%) Query: 15 GILIDLDGTVFRGNELIEGAREAIKTLRRMGKKIVFLSNRGNISRAMCRKKLLGAGIETD 74 G+LID+DG ++ G ELI GA + IK L F++N + +KL G GI+ + Sbjct: 4 GLLIDMDGVIYSGEELIFGADKFIKNLIDEDIPFAFMTNNSQRTALEVVRKLKGLGIKVE 63 Query: 75 VNDIVLSSSVTAAFLKKHYRFSKVWVLGEQGLVDELRLAGVQNASEPKEADWLVISLHET 134 + + S+ T FL +VLGE GL+ L G+ + + +++V+ Sbjct: 64 ESHVYTSAMATGKFLSDQSPAGTAYVLGEGGLLSSLHDHGITLVN--TDPEFVVLGEGRN 121 Query: 135 LTYDDLNQAFQAAAGGARIIATNKDRSFPNEDGNAIDVAGMIGAIETSAQAKTELVVGKP 194 T + + +A GA+ I TN+D S N + +A IE A + V GKP Sbjct: 122 FTLEMVQRAVDMILAGAKFITTNRDPSPKKPGWNNLGIAATTAMIE-EATGRKAFVTGKP 180 Query: 195 SWLMAEAACTAMGLSAHECMIIGDSIESDIAMGKLYGMKSALVLTGSAKQGEQRLYT--P 252 S +M +A +GL E +IGD++E+DI G G K+ LVL+G + + Y P Sbjct: 181 SPVMMRSARKFLGLETSETTVIGDTMETDIQGGVQMGYKTILVLSGISSKDTLGHYAFKP 240 Query: 253 DYVLDSIKDV 262 D + S+ ++ Sbjct: 241 DMIASSVDEI 250 Lambda K H 0.317 0.133 0.375 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 167 Number of extensions: 8 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 272 Length of database: 260 Length adjustment: 25 Effective length of query: 247 Effective length of database: 235 Effective search space: 58045 Effective search space used: 58045 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory